Contacts of the helix formed by residues 140 - 157 (chain B) in PDB entry 6GR2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLY* 4.0 2.8 - - - -
37B ARG* 2.7 47.6 + - - +
133B VAL* 4.2 0.4 - - - -
138B GLY* 3.3 4.9 - - - +
139B LEU* 1.3 80.2 - - - +
141B SER* 1.3 61.9 + - - +
142B SER* 3.2 6.5 - - - +
143B ALA* 4.0 13.9 - - - +
144B SER* 3.0 25.1 + - - -
186B ASP* 3.1 18.8 + - - -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 4.5 2.0 + - - -
131B SER* 5.4 1.1 - - - -
133B VAL* 3.6 25.7 - - - +
134B PRO 3.9 10.7 + - - -
135B LEU* 3.7 32.2 - - - +
136B GLY 3.8 7.4 + - - -
139B LEU 3.5 2.2 - - - -
140B SER* 1.3 75.2 - - - +
142B SER* 1.3 60.7 + - - +
144B SER* 3.5 3.5 - - - -
145B LEU* 2.8 31.9 + - - +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.7 35.8 - - - -
140B SER* 4.1 6.3 - - - +
141B SER* 1.3 82.3 + - - +
143B ALA* 1.3 65.7 + - - +
145B LEU* 3.2 7.6 + - - +
146B GLU* 2.9 36.2 + - - +
174B GLU* 3.7 16.7 + - - -
186B ASP* 5.3 2.8 + - - -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 3.7 9.9 + - - -
141B SER 3.4 0.4 - - - -
142B SER* 1.3 78.3 + - - +
144B SER* 1.3 61.6 + - - +
146B GLU* 3.4 15.9 - - - +
147B VAL* 2.8 36.4 + - - +
174B GLU* 5.0 0.2 - - - +
186B ASP* 3.6 44.2 - - + +
187B GLN* 3.9 9.6 - - - +
190B SER* 4.5 2.5 - - - -
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 2.7 29.1 + - - +
35B PRO 3.4 22.2 + - - -
36B GLY* 3.8 2.4 + - - -
61B THR* 2.9 21.3 + - - -
133B VAL* 4.1 2.7 - - - +
140B SER 3.0 21.0 + - - -
141B SER* 3.5 8.3 - - - -
143B ALA* 1.3 76.7 - - - +
145B LEU* 1.3 57.4 + - - +
148B ALA* 3.0 30.8 + - - +
190B SER* 4.0 4.8 + - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 4.0 10.7 + - + +
63B LEU* 5.4 1.1 - - + -
106B TRP* 4.1 22.0 - - + +
109B TYR* 4.1 26.2 - - + -
110B VAL* 4.6 9.6 - - + -
129B VAL* 3.7 38.1 - - + -
141B SER 2.8 17.5 + - - +
142B SER* 3.5 5.8 - - - +
144B SER* 1.3 77.1 - - - +
146B GLU* 1.3 56.9 + - - +
148B ALA* 3.4 1.4 + - + +
149B THR* 2.9 44.2 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TYR* 3.2 36.2 - - + +
113B VAL* 3.8 22.2 - - + +
142B SER 2.9 26.3 + - - +
143B ALA* 3.1 7.3 + - - +
145B LEU* 1.3 76.9 - - - +
147B VAL* 1.3 58.1 + - - +
149B THR* 3.3 5.3 + - - -
150B TYR* 2.9 27.2 + - - +
170B CYS* 3.4 24.9 - - + +
173B ALA* 5.4 0.9 - - + -
174B GLU* 2.6 29.3 - - - +
187B GLN* 3.2 25.6 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA* 4.0 3.6 - - + -
143B ALA 2.8 20.2 + - - +
146B GLU* 1.3 72.6 - - - +
148B ALA* 1.3 58.8 + - - +
150B TYR* 3.2 2.2 + - + +
151B THR* 2.7 37.8 + - - -
170B CYS* 4.0 19.1 - - + -
187B GLN* 3.9 28.5 - - + +
190B SER* 3.9 15.5 - - - +
191B LEU* 3.4 33.7 - - + +
387B ALA* 3.6 20.0 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 3.2 21.6 - - + +
34B ALA* 3.5 15.0 - - + +
61B THR* 3.9 26.2 - - + +
63B LEU* 4.0 10.1 - - + -
144B SER 3.0 19.4 + - - +
145B LEU 3.6 4.3 - - - +
146B GLU 3.3 0.2 - - - -
147B VAL* 1.3 77.2 - - - +
149B THR* 1.3 63.4 + - - +
151B THR 3.3 0.3 + - - -
152B PHE* 2.9 21.7 + - - +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 3.7 19.1 - - + +
110B VAL* 3.7 35.2 - - + +
113B VAL* 3.9 22.4 - - + -
114B ILE* 4.8 2.5 - - + -
125B PHE* 5.5 4.0 - - + -
145B LEU* 2.9 26.5 + - - +
146B GLU* 3.5 6.1 - - - -
148B ALA* 1.3 74.7 - - - +
150B TYR* 1.3 64.2 + - - +
152B PHE* 3.1 4.5 + - + +
153B LEU* 3.0 33.1 + - + +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.9 10.7 - - + +
117B TYR* 3.6 23.8 - + - -
118B PRO* 3.8 15.8 - - + +
146B GLU 2.9 14.6 + - - +
147B VAL* 3.6 8.3 - - + +
149B THR* 1.3 77.2 - - - +
151B THR* 1.3 63.9 + - - +
153B LEU* 3.2 7.4 + - - +
154B GLN* 3.1 39.9 + - + +
159B ASP* 2.2 31.5 + - - -
165B ALA* 5.1 1.6 - - - +
166B ARG* 3.2 37.1 + - + +
169B VAL* 3.8 36.5 - - + +
170B CYS* 4.0 14.4 - - - -
191B LEU* 5.5 2.5 - - + -
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 3.5 28.7 - - + -
147B VAL* 2.7 27.9 + - - +
148B ALA* 4.4 0.2 - - - -
150B TYR* 1.3 72.4 - - - +
152B PHE* 1.3 62.0 + - - +
154B GLN* 3.3 23.7 + - - +
155B GLN* 3.1 30.4 - - - +
191B LEU* 4.9 2.4 - - - +
387B ALA* 3.5 22.7 - - + +
388B LYS* 4.4 10.1 - - - +
389B VAL* 4.3 10.1 - - + -
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.6 34.1 - - + -
32B VAL* 3.8 12.5 - - + +
63B LEU* 4.0 28.3 - - + -
64B VAL 4.7 0.7 - - - -
65B GLY* 3.7 33.9 - - - -
66B SER 3.9 2.9 - - - -
125B PHE* 3.2 44.0 - + + -
127B ALA* 4.2 4.0 - - + -
148B ALA 2.9 12.9 + - - +
149B THR* 3.1 9.4 + - + +
151B THR* 1.3 77.0 - - - +
153B LEU* 1.3 62.0 + - + +
155B GLN* 2.8 30.3 + - + +
156B LEU* 3.3 22.1 + - + +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 4.2 10.3 - - + -
114B ILE* 4.1 19.3 - - + -
117B TYR* 3.6 42.0 - - + -
122B LEU* 4.1 18.6 - - + +
125B PHE* 3.7 35.4 - - + -
149B THR* 3.0 22.5 + - + +
150B TYR* 3.2 6.7 + - - +
152B PHE* 1.3 78.8 - - + +
154B GLN* 1.3 56.5 + - - +
156B LEU* 3.2 16.1 + - + +
157B CYS* 2.7 33.1 + - - +
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 3.3 17.7 + - - +
150B TYR* 3.1 41.6 + - + +
151B THR* 3.4 28.9 + - - +
152B PHE 3.1 0.4 - - - -
153B LEU* 1.3 76.5 - - - +
155B GLN* 1.3 67.0 + - - +
157B CYS 3.7 0.7 - - - -
158B PRO* 3.0 32.2 - - + +
159B ASP* 3.4 12.2 + - - +
166B ARG* 3.3 36.7 + - - +
191B LEU* 5.5 1.4 - - - +
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 4.1 34.9 - - + +
31B ALA 5.0 0.4 - - - +
32B VAL* 4.2 7.4 - - + -
151B THR* 3.1 18.5 - - - +
152B PHE* 2.8 19.3 + - + +
154B GLN* 1.3 86.3 + - - +
156B LEU* 1.3 62.7 + - - +
157B CYS 3.6 0.3 + - - -
158B PRO* 4.7 3.3 - - - +
389B VAL* 3.1 44.1 - - + +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.4 27.8 - - + -
67B PRO* 4.0 29.4 - - + -
121B PRO 4.7 0.9 - - - +
122B LEU* 4.4 2.5 - - + -
123B PRO* 3.8 33.0 - - + +
124B GLY 4.9 0.4 - - - +
125B PHE* 3.5 38.6 - - + -
152B PHE* 3.8 20.9 - - + +
153B LEU* 3.2 18.7 + - + +
155B GLN* 1.3 76.6 - - - +
157B CYS* 1.3 61.2 + - - +
158B PRO* 4.3 1.8 - - - +
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Residues in contact with CYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 2.6 30.8 + - + -
119B ALA* 3.7 9.0 - - - -
120B ALA* 3.5 35.9 - - - -
121B PRO* 3.5 26.5 - - - +
122B LEU* 3.8 17.7 - - + -
153B LEU 2.7 7.9 + - - +
154B GLN 3.3 2.2 - - - -
155B GLN 3.3 0.4 - - - -
156B LEU* 1.3 77.5 - - - +
158B PRO* 1.3 68.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il